From 9286dafe7477f2e0a34d7e67236d3e6005eb6457 Mon Sep 17 00:00:00 2001
From: Sasha Sherstnev <a.sherstnev@dundee.ac.uk>
Date: Thu, 24 Oct 2013 18:25:48 +0100
Subject: [PATCH] Modify servlet configuration

---
 WEB-INF/sun-jaxws.xml |   51 -------------------------------------------------
 WEB-INF/web.xml       |   39 +++++++++++++++++--------------------
 2 files changed, 18 insertions(+), 72 deletions(-)
 delete mode 100644 WEB-INF/sun-jaxws.xml

diff --git a/WEB-INF/sun-jaxws.xml b/WEB-INF/sun-jaxws.xml
deleted file mode 100644
index 13d6fac..0000000
--- a/WEB-INF/sun-jaxws.xml
+++ /dev/null
@@ -1,51 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<endpoints xmlns='http://java.sun.com/xml/ns/jax-ws/ri/runtime' version='2.0'>
-	<endpoint name='RegistryWS'
-		implementation='compbio.ws.server.RegistryWS'
-		url-pattern='/RegistryWS'/>
-	<endpoint name='ClustalWS'
-		implementation='compbio.ws.server.ClustalWS'
-		url-pattern='/ClustalWS'/>
-	<endpoint name='ClustalOWS'
-		implementation='compbio.ws.server.ClustalOWS'
-		url-pattern='/ClustalOWS'/>
-	<endpoint name='MuscleWS'
-		implementation='compbio.ws.server.MuscleWS'
-		url-pattern='/MuscleWS'/>
-	<endpoint name='TcoffeeWS'
-		implementation='compbio.ws.server.TcoffeeWS'
-		url-pattern='/TcoffeeWS'/>
-	<endpoint name='MafftWS'
-		implementation='compbio.ws.server.MafftWS'
-		url-pattern='/MafftWS'/>
-	<endpoint name='ProbconsWS'
-		implementation='compbio.ws.server.ProbconsWS'
-		url-pattern='/ProbconsWS'/>
-	<endpoint name='MSAprobsWS'
-		implementation='compbio.ws.server.MSAprobsWS'
-		url-pattern='/MSAprobsWS'/>
-	<endpoint name='GLprobsWS'
-		implementation='compbio.ws.server.GLprobsWS'
-		url-pattern='/GLprobsWS'/>
-	<endpoint name='AAConWS'
-		implementation='compbio.ws.server.AAConWS'
-		url-pattern='/AAConWS'/>
-	<endpoint name='JronnWS'
-		implementation='compbio.ws.server.JronnWS'
-		url-pattern='/JronnWS'/>
-	<endpoint name='DisemblWS'
-		implementation='compbio.ws.server.DisemblWS'
-		url-pattern='/DisemblWS'/>
-	<endpoint name='GlobPlotWS'
-		implementation='compbio.ws.server.GlobPlotWS'
-		url-pattern='/GlobPlotWS'/>
-	<endpoint name='IUPredWS'
-		implementation='compbio.ws.server.IUPredWS'
-		url-pattern='/IUPredWS'/>
-	<endpoint name='JpredWS'
-		implementation='compbio.ws.server.JpredWS'
-		url-pattern='/JpredWS'/>
-	<endpoint name='RNAalifoldWS'
-		implementation='compbio.ws.server.RNAalifoldWS'
-		url-pattern='/RNAalifoldWS'/>
-</endpoints>
diff --git a/WEB-INF/web.xml b/WEB-INF/web.xml
index cec1884..242a900 100644
--- a/WEB-INF/web.xml
+++ b/WEB-INF/web.xml
@@ -3,22 +3,16 @@
  xsi:schemaLocation="http://java.sun.com/xml/ns/j2ee http://java.sun.com/xml/ns/j2ee/web-app_2_4.xsd"
  version="2.4">
 
-<display-name>JABAWS</display-name>
-<description>JAva Bioinformatics Analysis Web Services (JABAWS) v.2</description>
+<display-name>ProteoCache</display-name>
+<description>ProteoCache - Results repository for the Dundee Resource</description>
 
+	<welcome-file-list>
+		<welcome-file>Index.jsp</welcome-file>
+	</welcome-file-list>
 
-	<!-- JABAWS listeners -->
+	<!-- ProteoCache listeners -->
 	<listener>
-		<listener-class>compbio.ws.server.MainManager</listener-class>
-	</listener>
-	<listener>
-		<listener-class>compbio.stat.servlet.StatisticCollector</listener-class>
-	</listener>
-	<listener>
-		<listener-class>compbio.ws.server.SetExecutableFlag</listener-class>
-	</listener>
-	<listener>
-		<listener-class>com.sun.xml.ws.transport.http.servlet.WSServletContextListener</listener-class>
+		<listener-class>compbio.listeners.ContextListener</listener-class>
 	</listener>
 
 
@@ -48,7 +42,8 @@
 	</servlet>
 
 
-	<!-- JABAWS servlets -->
+	<!-- ProteoCache servlets -->
+<!--
 	<servlet>
 		<description>Display pre-calculated accounting info</description>
 		<servlet-name>DisplayStat</servlet-name>
@@ -184,8 +179,12 @@
 		<servlet-class>com.sun.xml.ws.transport.http.servlet.WSServlet</servlet-class>
 		<load-on-startup>1</load-on-startup>
 	</servlet>
+-->
+
 
-	<!-- JABAWS servlet mappings -->
+
+	<!-- ProteoCache servlet mappings -->
+<!--
 	<servlet-mapping>
 		<servlet-name>listings</servlet-name>
 		<url-pattern>/</url-pattern>
@@ -305,9 +304,10 @@
 		<servlet-name>RNAalifoldWS</servlet-name>
 		<url-pattern>/RNAalifoldWS</url-pattern>
 	</servlet-mapping>
+-->
 
 
-	<!-- JABAWS security constraints -->
+	<!-- ProteoCache security constraints -->
 	<security-constraint>
 		<web-resource-collection>
 		<web-resource-name>Administrator pages</web-resource-name>
@@ -317,10 +317,8 @@
 			<url-pattern>/AnnualStat</url-pattern>
 			<url-pattern>/conf/*</url-pattern>
 			<url-pattern>/binaries/*</url-pattern>
-			<url-pattern>/jobsout/*</url-pattern>
 			<url-pattern>/testsrc/*</url-pattern>
 			<url-pattern>/lib/*</url-pattern>
-			<url-pattern>/test-output/*</url-pattern>
 			<!-- Uncomment this to secure services status checker 
 			<url-pattern>/HttpCodeResponseServiceStatus/*</url-pattern>
 			<url-pattern>/ServiceStatus</url-pattern>
@@ -346,17 +344,16 @@
 		<auth-constraint/>
 	</security-constraint>
 
-
 	<!-- Define the Login Configuration for this Application -->
 	<login-config>
 		<auth-method>BASIC</auth-method>
-		<realm-name>JABAWS administrators</realm-name>
+		<realm-name>ProteCache administrators</realm-name>
 	</login-config>
 
 
 	<!-- Security roles referenced by this web application -->
 	<security-role>
-		<description>The role that is required to log in and view JABAWS internals</description>
+		<description>The role that is required to log in and view ProteCache internals</description>
 		<role-name>admin</role-name>
 	</security-role>
 
-- 
1.7.10.2